Genomic Characterisation of a Highly Divergent Siadenovirus (Psittacine Siadenovirus F) from the Critically Endangered Orange-Bellied Parrot (Neophema chrysogaster)

Abstract

Siadenoviruses have been detected in wild and captive birds worldwide. Only nine siadenoviruses have been fully sequenced; however, partial sequences for 30 others, many of these from wild Australian birds, are also described. Some siadenoviruses, e.g., the turkey siadenovirus A, can cause disease; however, most cause subclinical infections. An example of a siadenovirus causing predominately subclinical infections is psittacine siadenovirus 2, proposed name psittacine siadenovirus F (PsSiAdV-F), which is enzootic in the captive breeding population of the critically endangered orange-bellied parrot (OBP, Neophema chrysogaster). Here, we have fully characterised PsSiAdV-F from an OBP. The PsSiAdV-F genome is 25,392 bp in length and contained 25 putative genes. The genome architecture of PsSiAdV-F exhibited characteristics similar to members within the genus Siadenovirus; however, the novel PsSiAdV-F genome was highly divergent, showing highest and lowest sequence similarity to skua siadenovirus A (57.1%) and psittacine siadenovirus D (31.1%), respectively. Subsequent phylogenetic analyses of the novel PsSiAdV-F genome positioned the virus into a phylogenetically distinct sub-clade with all other siadenoviruses and did not show any obvious close evolutionary relationship. Importantly, the resulted tress continually demonstrated that novel PsSiAdV-F evolved prior to all known members except the frog siadenovirus A in the evolution and possibly the ancestor of the avian siadenoviruses. To date, PsSiAdV-F has not been detected in wild parrots, so further studies screening PsSiAdV-F in wild Australian parrots and generating whole genome sequences of siadenoviruses of Australian native passerine species is recommended to fill the siadenovirus evolutionary gaps.

Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

“…1 ) that is basal to all known avian siadenoviruses. This suggests that all the avian siadenoviruses evolved from the ancestral bird that gave rise to PsSiAdV-F, which is consistent with a recent study that reported that PsSiAdV-F was basal to all avian siadenoviruses 20 . Evidence that this ancestral species may have been a primitive Australian or African parrot includes the observation that PsSiAdV-F has only been detected in psittacine species where it causes predominantly subclinical infections.…”

“…The main aims of this study were not only to understand the virome structure of apparently healthy Australian Neophema birds but also to track the evolutionary history of a recently sequenced PsSiAdV-F in the critically endangered Australian parrot, the orange-bellied parrot ( Neophema chrysogaster ) 20 . Notably, the PsSiAdV-F sequenced from this study was very similar (a nucleotide identity of > 99% at genome level) to the recently sequenced two PsSiAdV-F strains of OBP2209 and WVL19065-01E from the orange-bellied parrot and African grey parrot ( Psittacus erithacus ), respectively, and phylogenetically all the three strains of PsSiAdV-F were positioned in a monophyletic subclade (100% bootstrap support ) (Fig.…”

“…Evidence that this ancestral species may have been a primitive Australian or African parrot includes the observation that PsSiAdV-F has only been detected in psittacine species where it causes predominantly subclinical infections. The PsSiAdV-F is also widespread in captive populations of at least three species of Australian parrot: the orange-bellied parrot ( Neophema chrysogaster ), the scarlet-chested parrot ( Neophema splendida ) and the Bourke’s parrot ( Neopsephotus bourkii ) 20 , 49 , 50 . The finding that PsSiAdV-F originated in Australian psittacine birds needs to be confirmed by it being identified in other Australian psittacine species, and, to date, surveys of psittacine birds in Australia have not detected it.…”

“…In addition, a psittacine siadenovirus F (PsSiAdV-F) has recently been characterised from the critically endangered, orange-bellied parrot ( Neophema chrysogaster ) 20 . Subsequent phylogenetic analyses demonstrated that novel PsSiAdV-F infecting orange-bellied parrot evolved prior to all known members of siadenoviruses except the frog siadenovirus A, and did not show any obvious close evolutionary relationship 20 .…”

“…In addition, a psittacine siadenovirus F (PsSiAdV-F) has recently been characterised from the critically endangered, orange-bellied parrot ( Neophema chrysogaster ) 20 . Subsequent phylogenetic analyses demonstrated that novel PsSiAdV-F infecting orange-bellied parrot evolved prior to all known members of siadenoviruses except the frog siadenovirus A, and did not show any obvious close evolutionary relationship 20 . Therefore, the aims of this study were not only to identify the known and unknown viruses that may exist in the two species of Neophema birds but also to track the evolutionary relationships of recently emerging PsSiAdV-F circulating in the critically endangered, orange-bellied parrot.…”